"In contrast there are masters in the martial arts who learned their art as a means of survival and became masters in a realistic and hostile environment. We don’t have anyone like this in the programming profession, or at least I haven’t met any."
Jamie Zawinski. Jeff Dean and a lot of the other early Google employees, many of whom aren't well known outside the company. Dave Cutler, Steve Wozniak, Doug Cutting, John Carmack.
"As a UC Berkeley graduate student, Joy worked for Fabry's Computer Systems Research Group CSRG in managing the BSD support and rollout where many claim he was largely responsible for managing the authorship of BSD UNIX, from which sprang many modern forms of UNIX, including FreeBSD, NetBSD, and OpenBSD. Apple Inc. has based much of the Mac OS X kernel and OS Services on the BSD technology.
Some of his most notable contributions were the vi editor, NFS, and csh. Joy's prowess as a computer programmer is legendary, with an oft-told anecdote that he wrote the vi editor in a weekend. Joy denies this assertion.[2]"
Ward Cunningham, Don Knuth (mentioned in the OP) and Linus Torvalds also qualify, as well, I think. Note that I'm not simply listing out random famous software people. I don't think Martin Fowler qualifies, for instance.
The OP brought up and specifically disqualified Don Knuth because he had freedom as an academic that working software developers don't. The example given was his ability to take off 3 years to work on TeX.
By those criteria I consider Linus Torvalds likely to be disqualified as well since he made his reputation while using the freedom he had as a student.
Ward Cunningham would be a good addition to the list.
I wonder how Don Knuth would fare writing something like TeX under time constraints. I suspect that most programmers would prefer to have unlimited time to make things "perfect" rather than be under pressure; just because Knuth had the liberty to take that option doesn't mean he wouldn't do as well as (if not better than) anyone else on a restricted schedule.
I second that. I also think that a person who quitted using email in 1990 for not loosing time for his studies, wouldn't have unlimited time for writing Tex.
I think maybe Peter Norvig would qualify.
http://en.wikipedia.org/wiki/Peter_Norvig